# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:43:21 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (8R,9S,13S,14S,17R)-5',5',13-trimethyl-6'-oxo-3',4',5',6,6',7,8,9,11,12,13,14,15,16-tetradecahydrospiro[cyclopenta[a]phenanthrene-17,2'-pyran]-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CC[C@@]2(CC[C@H]3[C@@H]4CCc5cc(ccc5[C@H]4CC[C@]23C)C(N)=O)OC1=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 E04  E04  (8R,9S,13S,14S,17R)-5',5',13-trimethyl-6'-oxo-3',4',5',6,6',7,8,9,11,12,13,14,15,16-tetradecahydrospiro[cyclopenta[a]phenanthrene-17,2'-pyran]-3-carboxamide  ligand  62  29  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_E04
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 E04  O26   O  O     0  -0.447   5.7078   0.8164   1.9328
 E04  C20   C  C     0   0.577   5.0776   0.5830   0.9293
 E04  C21   C  CT    0  -0.248   5.6484   0.7970  -0.4608
 E04  C25   C  CH3   0  -0.638   7.1182   0.3828  -0.4885
 E04  C24   C  CH3   0  -0.646   5.5442   2.3065  -0.7442
 E04  C22   C  CH2   0  -0.428   4.8642   0.0015  -1.5038
 E04  C23   C  CH2   0  -0.503   3.3678   0.1581  -1.3109
 E04  C17   C  CT    0   0.309   2.9459  -0.3466   0.0638
 E04  O19   O  O2    0  -0.469   3.8144   0.2050   1.0762
 E04  C13   C  CT    0  -0.092   1.4804  -0.0167   0.4584
 E04  C18   C  CH3   0  -0.669   1.3167  -0.2026   1.9757
 E04  C14   C  CH1   0  -0.200   0.7327  -1.1013  -0.3316
 E04  C15   C  CH2   0  -0.448   1.5218  -2.3774  -0.0409
 E04  C16   C  CH2   0  -0.476   2.9793  -1.8966   0.1297
 E04  C8    C  CH1   0  -0.241  -0.7658  -1.0885  -0.0831
 E04  C9    C  CH1   0  -0.267  -1.3148   0.2913  -0.4809
 E04  C11   C  CH2   0  -0.449  -0.5831   1.4242   0.2520
 E04  C12   C  CH2   0  -0.429   0.9333   1.3484   0.0505
 E04  C10   C  CR6   0   0.121  -2.8252   0.3474  -0.3522
 E04  C1    C  CR16  0  -0.308  -3.4920   1.5715  -0.2753
 E04  C2    C  CR16  0  -0.288  -4.8702   1.6512  -0.1869
 E04  C3    C  CR6   0  -0.041  -5.6357   0.4880  -0.1809
 E04  C27   C  C     0   0.488  -7.1288   0.4893  -0.1115
 E04  O29   O  O     0  -0.485  -7.7809  -0.4817  -0.4743
 E04  N28   N  NH2   0  -0.817  -7.7036   1.6055   0.3626
 E04  C4    C  CR16  0  -0.324  -4.9806  -0.7323  -0.2810
 E04  C5    C  CR6   0   0.082  -3.5949  -0.8237  -0.3588
 E04  C6    C  CH2   0  -0.508  -2.9688  -2.1931  -0.4302
 E04  C7    C  CH2   0  -0.429  -1.5095  -2.1684  -0.8539
 E04  H251  H  HCH3  0   0.238   7.7192   0.9665   0.2069
 E04  H252  H  HCH3  0   0.235   7.2422  -0.6734  -0.2451
 E04  H253  H  HCH3  0   0.233   7.5167   0.5416  -1.4918
 E04  H241  H  HCH3  0   0.242   5.9351   2.5118  -1.7418
 E04  H242  H  HCH3  0   0.240   4.5171   2.6711  -0.7078
 E04  H243  H  HCH3  0   0.245   6.1290   2.8828  -0.0274
 E04  H221  H  HCH2  0   0.252   5.1533   0.3442  -2.4997
 E04  H222  H  HCH2  0   0.244   5.1497  -1.0534  -1.4496
 E04  H231  H  HCH2  0   0.255   3.0962   1.2068  -1.4433
 E04  H232  H  HCH2  0   0.265   2.8320  -0.3959  -2.0824
 E04  H181  H  HCH3  0   0.235   0.2698  -0.2219   2.2727
 E04  H182  H  HCH3  0   0.237   1.7630  -1.1281   2.3400
 E04  H183  H  HCH3  0   0.237   1.7815   0.6207   2.5183
 E04  H14   H  HCH1  0   0.225   0.8572  -0.8717  -1.3992
 E04  H151  H  HCH2  0   0.241   1.4255  -3.1120  -0.8404
 E04  H152  H  HCH2  0   0.229   1.1634  -2.8555   0.8737
 E04  H161  H  HCH2  0   0.248   3.6292  -2.3076  -0.6442
 E04  H162  H  HCH2  0   0.253   3.3918  -2.2235   1.0850
 E04  H8    H  HCH1  0   0.223  -0.9629  -1.2534   0.9837
 E04  H9    H  HCH1  0   0.239  -1.0884   0.4122  -1.5516
 E04  H111  H  HCH2  0   0.243  -0.9166   2.3932  -0.1219
 E04  H112  H  HCH2  0   0.229  -0.8403   1.4024   1.3146
 E04  H121  H  HCH2  0   0.228   1.1326   1.5312  -1.0083
 E04  H122  H  HCH2  0   0.233   1.4237   2.1542   0.6043
 E04  H1    H  HCR6  0   0.249  -2.9286   2.4946  -0.2938
 E04  H2    H  HCR6  0   0.251  -5.3288   2.6313  -0.1495
 E04  H281  H  HNH2  0   0.412  -7.1788   2.3521   0.7822
 E04  H282  H  HNH2  0   0.404  -8.7062   1.6539   0.4414
 E04  H4    H  HCR6  0   0.248  -5.5655  -1.6446  -0.2937
 E04  H61   H  HCH2  0   0.250  -3.5541  -2.8254  -1.1020
 E04  H62   H  HCH2  0   0.246  -3.0432  -2.6596   0.5580
 E04  H71   H  HCH2  0   0.220  -1.4238  -1.9786  -1.9295
 E04  H72   H  HCH2  0   0.243  -1.0674  -3.1499  -0.6707

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 E04  O26  C20   double    1.208  0.020  1.208
 E04  C20  C21   single    1.518  0.020  1.518
 E04  C20  O19   single    1.327  0.020  1.327
 E04  C21  C25   single    1.527  0.020  1.527
 E04  C21  C24   single    1.539  0.020  1.539
 E04  C21  C22   single    1.528  0.020  1.528
 E04  C25  H251  single    0.970  0.020  1.090
 E04  C25  H252  single    0.970  0.020  1.090
 E04  C25  H253  single    0.970  0.020  1.090
 E04  C24  H241  single    0.970  0.020  1.090
 E04  C24  H242  single    0.970  0.020  1.090
 E04  C24  H243  single    0.970  0.020  1.090
 E04  C22  C23   single    1.517  0.020  1.517
 E04  C22  H221  single    0.970  0.020  1.090
 E04  C22  H222  single    0.970  0.020  1.090
 E04  C23  C17   single    1.524  0.020  1.524
 E04  C23  H231  single    0.970  0.020  1.090
 E04  C23  H232  single    0.970  0.020  1.090
 E04  C17  O19   single    1.443  0.020  1.443
 E04  C17  C13   single    1.553  0.020  1.553
 E04  C17  C16   single    1.552  0.020  1.552
 E04  C13  C18   single    1.537  0.020  1.537
 E04  C13  C14   single    1.536  0.020  1.536
 E04  C13  C12   single    1.526  0.020  1.526
 E04  C18  H181  single    0.970  0.020  1.090
 E04  C18  H182  single    0.970  0.020  1.090
 E04  C18  H183  single    0.970  0.020  1.090
 E04  C14  C15   single    1.528  0.020  1.528
 E04  C14  C8    single    1.519  0.020  1.519
 E04  C14  H14   single    0.970  0.020  1.090
 E04  C15  C16   single    1.544  0.020  1.544
 E04  C15  H151  single    0.970  0.020  1.090
 E04  C15  H152  single    0.970  0.020  1.090
 E04  C16  H161  single    0.970  0.020  1.090
 E04  C16  H162  single    0.970  0.020  1.090
 E04  C8   C9    single    1.537  0.020  1.537
 E04  C8   C7    single    1.521  0.020  1.521
 E04  C8   H8    single    0.970  0.020  1.090
 E04  C9   C11   single    1.535  0.020  1.535
 E04  C9   C10   single    1.517  0.020  1.517
 E04  C9   H9    single    0.970  0.020  1.090
 E04  C11  C12   single    1.532  0.020  1.532
 E04  C11  H111  single    0.970  0.020  1.090
 E04  C11  H112  single    0.970  0.020  1.090
 E04  C12  H121  single    0.970  0.020  1.090
 E04  C12  H122  single    0.970  0.020  1.090
 E04  C10  C1    aromatic  1.396  0.020  1.396
 E04  C10  C5    aromatic  1.401  0.020  1.401
 E04  C1   C2    aromatic  1.383  0.020  1.383
 E04  C1   H1    single    0.930  0.020  1.080
 E04  C2   C3    aromatic  1.393  0.020  1.393
 E04  C2   H2    single    0.930  0.020  1.080
 E04  C3   C27   single    1.495  0.020  1.495
 E04  C3   C4    aromatic  1.389  0.020  1.389
 E04  C27  O29   double    1.225  0.020  1.225
 E04  C27  N28   single    1.342  0.020  1.342
 E04  N28  H281  single    0.860  0.020  1.020
 E04  N28  H282  single    0.860  0.020  1.020
 E04  C4   C5    aromatic  1.391  0.020  1.391
 E04  C4   H4    single    0.930  0.020  1.080
 E04  C5   C6    single    1.507  0.020  1.507
 E04  C6   C7    single    1.520  0.020  1.520
 E04  C6   H61   single    0.970  0.020  1.090
 E04  C6   H62   single    0.970  0.020  1.090
 E04  C7   H71   single    0.970  0.020  1.090
 E04  C7   H72   single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 E04  O19   C20  C21   119.97  3.000
 E04  O19   C20  O26   117.38  3.000
 E04  C21   C20  O26   122.51  3.000
 E04  C22   C21  C24   110.49  3.000
 E04  C22   C21  C25   109.90  3.000
 E04  C24   C21  C25   109.13  3.000
 E04  C22   C21  C20   111.02  3.000
 E04  C24   C21  C20   106.34  3.000
 E04  C25   C21  C20   109.89  3.000
 E04  H253  C25  H252  107.73  3.000
 E04  H253  C25  H251  107.92  3.000
 E04  H252  C25  H251  108.29  3.000
 E04  H253  C25  C21   109.19  3.000
 E04  H252  C25  C21   111.59  3.000
 E04  H251  C25  C21   111.98  3.000
 E04  H243  C24  H242  107.85  3.000
 E04  H243  C24  H241  108.04  3.000
 E04  H242  C24  H241  107.77  3.000
 E04  H243  C24  C21   111.17  3.000
 E04  H242  C24  C21   112.67  3.000
 E04  H241  C24  C21   109.18  3.000
 E04  H222  C22  H221  106.17  3.000
 E04  H222  C22  C23   110.53  3.000
 E04  H221  C22  C23   110.16  3.000
 E04  H222  C22  C21   109.52  3.000
 E04  H221  C22  C21   108.85  3.000
 E04  C23   C22  C21   111.45  3.000
 E04  H232  C23  H231  106.27  3.000
 E04  H232  C23  C17   109.51  3.000
 E04  H231  C23  C17   111.02  3.000
 E04  H232  C23  C22   110.01  3.000
 E04  H231  C23  C22   109.23  3.000
 E04  C17   C23  C22   110.71  3.000
 E04  C16   C17  C13   102.81  3.000
 E04  C16   C17  O19   109.81  3.000
 E04  C13   C17  O19   107.96  3.000
 E04  C16   C17  C23   111.30  3.000
 E04  C13   C17  C23   114.84  3.000
 E04  O19   C17  C23   109.85  3.000
 E04  C17   O19  C20   127.17  3.000
 E04  C12   C13  C14   108.64  3.000
 E04  C12   C13  C18   109.50  3.000
 E04  C14   C13  C18   111.74  3.000
 E04  C12   C13  C17   117.41  3.000
 E04  C14   C13  C17   100.29  3.000
 E04  C18   C13  C17   109.00  3.000
 E04  H183  C18  H182  107.48  3.000
 E04  H183  C18  H181  106.71  3.000
 E04  H182  C18  H181  106.71  3.000
 E04  H183  C18  C13   110.77  3.000
 E04  H182  C18  C13   112.89  3.000
 E04  H181  C18  C13   111.96  3.000
 E04  H14   C14  C8    105.59  3.000
 E04  H14   C14  C15   107.50  3.000
 E04  C8    C14  C15   119.03  3.000
 E04  H14   C14  C13   107.28  3.000
 E04  C8    C14  C13   112.96  3.000
 E04  C15   C14  C13   103.92  3.000
 E04  H152  C15  H151  106.87  3.000
 E04  H152  C15  C16   110.69  3.000
 E04  H151  C15  C16   111.98  3.000
 E04  H152  C15  C14   110.81  3.000
 E04  H151  C15  C14   112.19  3.000
 E04  C16   C15  C14   104.38  3.000
 E04  H162  C16  H161  106.45  3.000
 E04  H162  C16  C15   111.13  3.000
 E04  H161  C16  C15   111.50  3.000
 E04  H162  C16  C17   110.16  3.000
 E04  H161  C16  C17   111.03  3.000
 E04  C15   C16  C17   106.62  3.000
 E04  H8    C8   C7    107.35  3.000
 E04  H8    C8   C9    108.80  3.000
 E04  C7    C8   C9    109.36  3.000
 E04  H8    C8   C14   109.57  3.000
 E04  C7    C8   C14   113.17  3.000
 E04  C9    C8   C14   108.51  3.000
 E04  H9    C9   C10   106.45  3.000
 E04  H9    C9   C11   106.58  3.000
 E04  C10   C9   C11   114.01  3.000
 E04  H9    C9   C8    106.07  3.000
 E04  C10   C9   C8    111.52  3.000
 E04  C11   C9   C8    111.64  3.000
 E04  H112  C11  H111  106.19  3.000
 E04  H112  C11  C12   111.08  3.000
 E04  H111  C11  C12   107.55  3.000
 E04  H112  C11  C9    109.71  3.000
 E04  H111  C11  C9    110.26  3.000
 E04  C12   C11  C9    111.88  3.000
 E04  H122  C12  H121  106.59  3.000
 E04  H122  C12  C11   109.93  3.000
 E04  H121  C12  C11   107.45  3.000
 E04  H122  C12  C13   111.27  3.000
 E04  H121  C12  C13   110.06  3.000
 E04  C11   C12  C13   111.35  3.000
 E04  C5    C10  C1    118.08  3.000
 E04  C5    C10  C9    121.03  3.000
 E04  C1    C10  C9    120.84  3.000
 E04  H1    C1   C2    118.09  3.000
 E04  H1    C1   C10   119.91  3.000
 E04  C2    C1   C10   122.00  3.000
 E04  H2    C2   C3    121.54  3.000
 E04  H2    C2   C1    118.45  3.000
 E04  C3    C2   C1    119.99  3.000
 E04  C4    C3   C27   118.38  3.000
 E04  C4    C3   C2    118.32  3.000
 E04  C27   C3   C2    123.27  3.000
 E04  N28   C27  O29   122.42  3.000
 E04  N28   C27  C3    116.42  3.000
 E04  O29   C27  C3    121.16  3.000
 E04  H282  N28  H281  116.86  3.000
 E04  H282  N28  C27   119.61  3.000
 E04  H281  N28  C27   122.82  3.000
 E04  H4    C4   C5    118.80  3.000
 E04  H4    C4   C3    119.07  3.000
 E04  C5    C4   C3    122.12  3.000
 E04  C6    C5   C4    118.43  3.000
 E04  C6    C5   C10   122.09  3.000
 E04  C4    C5   C10   119.47  3.000
 E04  H62   C6   H61   105.78  3.000
 E04  H62   C6   C7    108.88  3.000
 E04  H61   C6   C7    110.63  3.000
 E04  H62   C6   C5    108.42  3.000
 E04  H61   C6   C5    109.41  3.000
 E04  C7    C6   C5    113.40  3.000
 E04  H72   C7   H71   106.78  3.000
 E04  H72   C7   C6    109.11  3.000
 E04  H71   C7   C6    110.59  3.000
 E04  H72   C7   C8    110.81  3.000
 E04  H71   C7   C8    109.65  3.000
 E04  C6    C7   C8    109.86  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 E04  CONST_01  C3    C2   C1   C10     0.00   0.0  0
 E04  CONST_02  C3    C4   C5   C10     0.00   0.0  0
 E04  CONST_03  C4    C5   C10  C1      0.00   0.0  0
 E04  CONST_04  C4    C3   C2   C1      0.00   0.0  0
 E04  CONST_05  C5    C10  C1   C2      0.00   0.0  0
 E04  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 E04  CONST_07  C27   C3   C2   C1    180.00   0.0  0
 E04  CONST_08  C5    C4   C3   C27   180.00   0.0  0
 E04  CONST_09  H1    C1   C10  C9      0.00   0.0  0
 E04  CONST_10  H2    C2   C1   C10   180.00   0.0  0
 E04  CONST_11  H4    C4   C5   C10   180.00   0.0  0
 E04  CONST_12  H281  N28  C27  C3      0.00   0.0  0
 E04  CONST_13  H282  N28  C27  C3    180.00   0.0  0
 E04  Var_01    C23   C22  C21  C20    45.95  30.0  1
 E04  Var_02    C17   C23  C22  C21   -60.37  30.0  1
 E04  Var_03    O19   C20  C21  C22   -23.68  30.0  1
 E04  Var_04    C14   C15  C16  C17     5.27  30.0  1
 E04  Var_05    C9    C11  C12  C13   -54.87  30.0  1
 E04  Var_06    C5    C6   C7   C8     45.88  30.0  1
 E04  Var_07    C7    C6   C5   C10   -15.09  30.0  1
 E04  Var_08    O29   C27  C3   C2    159.45  30.0  2
 E04  Var_09    H251  C25  C21  C20   -60.52  30.0  3
 E04  Var_10    H241  C24  C21  C20  -179.45  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 E04  chir_01  C17  O19  C13  C16  positiv
 E04  chir_02  C13  C17  C14  C12  positiv
 E04  chir_03  C14  C13  C15  C8   negativ
 E04  chir_04  C8   C14  C9   C7   negativ
 E04  chir_05  C9   C8   C11  C10  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 E04  plan-1  C3    0.020
 E04  plan-1  C27   0.020
 E04  plan-1  O29   0.020
 E04  plan-1  N28   0.020
 E04  plan-1  H281  0.020
 E04  plan-1  H282  0.020
 E04  plan-2  C9    0.020
 E04  plan-2  C10   0.020
 E04  plan-2  C1    0.020
 E04  plan-2  C2    0.020
 E04  plan-2  C3    0.020
 E04  plan-2  C27   0.020
 E04  plan-2  C4    0.020
 E04  plan-2  C5    0.020
 E04  plan-2  C6    0.020
 E04  plan-2  H1    0.020
 E04  plan-2  H2    0.020
 E04  plan-2  H4    0.020
 E04  plan-3  O26   0.020
 E04  plan-3  C20   0.020
 E04  plan-3  C21   0.020
 E04  plan-3  O19   0.020

